Summer Research Opportunity In
Computational Biology
B B S I
@ P I T T 2 0 0 8
“Simulation and
Computer Visualization of Biological Systems at Multiple Scales”
An NIH-NSF Bioengineering & Bioinformatics Summer Institute (BBSI)
For Undergraduate and Graduate Students
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Overview
The BBSI @ Pitt
provides a unique training experience to students wishing to explore
the field of computational biology by providing an opportunity for
talented students to learn quantitative computer modeling methods at
multiple scales in the Life Sciences (molecular to cellular).
Students will attend classes taught by core faculty, and will have a
unique opportunity to work with leading scientists and subsequently
apply their knowledge towards a mentored state-of-the-art research
project of their choice.
The BBSI @ Pitt is a
joint program offered by the University of Pittsburgh, the
Pittsburgh Supercomputing Center, Duquesne University, and Carnegie
Mellon University. Program Dates
Coursework Topics
Math
and Biochemistry Review
Program Eligibility The program is open to all U.S. citizens and permanent residents. Applications from students in the life sciences, mathematics, engineering, and computer science are welcome. A total of 13 students will be admitted: 11 undergraduate students entering their junior or senior years, and 2 graduate students entering the first two years of graduate school will be admitted. Applications from students representing minority groups are highly encouraged. |
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Core
Instructors
Ivet
Bahar, PhD,
Program Director, Department of Computational Biology,
University of Pittsburgh
Takis Benos, PhD, Department of
Computational Biology, University of Pittsburgh
Rob
Coalson, PhD,
Departments of Chemistry and Physics, University of
Pittsburgh
G. Bard
Ermentrout, PhD,
Department of Mathematics, University of Pittsburgh
Jeffry
Madura, PhD,
Department of Chemistry and Biochemistry, Duquesne
University
Hagai
Meirovitch, PhD, Department of Computational Biology, University of
Pittsburgh
Joel
Stiles, MD/PhD,
Mellon College of Science & Pittsburgh Supercomputing
Center, Carnegie Mellon University
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To make this model, a single active zone geometry was created with computer-aided design software based on electron microscope measurements. The geometry was imported into DReAMM, replicated and edited, and then exported to MCell to run the simulation. The simulation results were then reimported into DReAMM for visualization and animation. Cyan spheres are synaptic vesicles with occupied (red) and unoccupied (blue) calcium binding sites. Calcium ions (yellow) enter through the transmembrane ion channels (black, closed; white, open) and can also bind to many intrinsic buffer sites (magenta). Image courtesy: Dr. Joel Stiles, Director, Center for Quantitative Biological Simulation, Pittsburgh Supercomputing Center (www.mcell.psc.edu).
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